An assay for RNA oxidation induced abasic sites using the Aldehyde Reactive Probe

References

• Hofer T, Marzetti E, Xu J, Seo AY, Gulec S, Knutson MD, Leeuwenburgh C, Dupont-Versteegden EE. Increased iron content and RNA oxidative damage in skeletal muscle with aging and disuse atrophy. Exp Gerontol 2008;43: 563–570.
   PubMed Web of Science ®Google Scholar
• Liu J, Head E, Gharib AM, Yuan W, Ingersoll RT, Hagen TM, Cotman CW, Ames BN. Memory loss in old rats is associated with brain mitochondrial decay and RNA/DNA oxidation: partial reversal by feeding acetyl-L-carnitine and/or R-alpha -lipoic acid. Proc Natl Acad Sci USA 2002;99: 2356–2361.
   PubMed Web of Science ®Google Scholar
• Martinet W, de Meyer GR, Herman AG, Kockx MM. Reactive oxygen species induce RNA damage in human atherosclerosis. European J Clin Investigat 2004;34:323–327.
   PubMed Web of Science ®Google Scholar
• Nunomura A, Chiba S, Kosaka K, Takeda A, Castellani RJ, Smith MA, Perry G. Neuronal RNA oxidation is a prominent feature of dementia with Lewy bodies. [Erratum appears in Neuroreport. 2003 Feb 10;14(2):293.]. Neuroreport 2002;13: 2035–2039.
   PubMed Web of Science ®Google Scholar
• Zhang J, Perry G, Smith MA, Robertson D, Olson SJ, Graham DG, Montine TJ. Parkinson's disease is associated with oxidative damage to cytoplasmic DNA and RNA in substantia nigra neurons. Am J Pathol 1999;154: 1423–1429.
   PubMed Web of Science ®Google Scholar
• Chang Y, Kong Q, Shan X, Tian G, Ilieva H, Cleveland DW, Rothstein JD, Borchelt DR, Wong PC, Lin CL. Messenger RNA oxidation occurs early in disease pathogenesis and promotes motor neuron degeneration in ALS. PLoS ONE 2008;3:e2849.
   PubMed Web of Science ®Google Scholar
• Nunomura A, Perry G, Hirai K, Aliev G, Takeda A, Chiba S, Smith MA. Neuronal RNA oxidation in Alzheimer's disease and Down's syndrome. Ann N Y Acad Sci 1999;893: 362–364.
   PubMed Web of Science ®Google Scholar
• Shan X, Tashiro H, Lin CL. The identification and characterization of oxidized RNAs in Alzheimer's disease. J Neurosci 2003;23:4913–4921.
   PubMed Web of Science ®Google Scholar
• Ding Q, Markesbery WR, Chen Q, Li F, Keller JN. Ribosome dysfunction is an early event in Alzheimer's disease. J Neurosci 2005;25:9171–9175.
   PubMed Web of Science ®Google Scholar
• Lovell MA, Markesbery WR. Oxidative damage in mild cognitive impairment and early Alzheimer's disease. J Neurosci Res 2007;85:3036–3040
   PubMed Web of Science ®Google Scholar
• Kong Q, Shan X, Chang Y, Tashiro H, Lin CL. RNA oxidation: a contributing factor or an epiphenomenon in the process of neurodegeneration. Free Radic Res 2008;42: 773–777.
   PubMed Web of Science ®Google Scholar
• Floyd RA, Watson JJ, Wong PK, Altmiller DH, Rickard RC. Hydroxyl free radical adduct of deoxyguanosine: sensitive detection and mechanisms of formation. Free Radic Res Commun 1986;1:163–172.
   PubMedGoogle Scholar
• Degan P, Shigenaga MK, Park EM, Alperin PE, Ames BN. Immunoaffinity isolation of urinary 8-hydroxy-2′-deoxyguanosine and 8-hydroxyguanine and quantitation of 8-hydroxy-2′-deoxyguanosine in DNA by polyclonal antibodies. Carcinogenesis 1991;12:865–871.
   PubMed Web of Science ®Google Scholar
• Dizdaroglu M. Chemical determination of free radical-induced damage to DNA. Free Radic Biol Med 1991;10:225–242.
   PubMed Web of Science ®Google Scholar
• Evans MD, Dizdaroglu M, Cooke MS. Oxidative DNA damage and disease: induction, repair and significance. Mutat Res 2004;567:1–61.
   PubMed Web of Science ®Google Scholar
• Yanagawa H, Ogawa Y, Ueno M. Redox ribonucleosides. Isolation and characterization of 5-hydroxyuridine, 8-hydroxyguanosine, and 8-hydroxyadenosine from Torula yeast RNA. J Biol Chem 1992;267:13320–13326.
   PubMed Web of Science ®Google Scholar
• Ide H, Akamatsu K, Kimura Y, Michiue K, Makino K, Asaeda A, Takamori Y, Kubo K. Synthesis and damage specificity of a novel probe for the detection of abasic sites in DNA. Biochemistry 1993;32:8276–8283.
   PubMed Web of Science ®Google Scholar
• Nakamura J, Swenberg JA. Endogenous apurinic/apyrimidinic sites in genomic DNA of mammalian tissues. Cancer Res 1999;59:2522–2526.
   PubMed Web of Science ®Google Scholar
• Thiebe R, Zachau HG. A specific modification next to the anticodon of phenylalanine transfer ribonucleic acid. Eur J Biochem 1968;5:546–555.
   PubMedGoogle Scholar
• Nishikawa K, Adams BL, Hecht SM. Chemical excision of apurinic acids from RNA. A Structurally Modified yeast tRNAPhe. J Am Chem Soc 1982;104:326–328.
   Google Scholar
• Kupfer PA, Leumann CJ. The chemical stability of abasic RNA compared to abasic DNA. Nucl Acids Res 2007;35:58–68.
   Google Scholar
• Pitsch S, Weiss PA. Chemical synthesis of RNA sequences with 2′-O-[(triisopropylsilyl)oxy]methyl-protected ribonucleoside phosphoramidites. Curr Protoc Nucleic Acid Chem 2002;Chapter 3:3.8.1–3.8.15.
   Google Scholar
• Crain PF. Preparation and enzymatic hydrolysis of DNA and RNA for mass spectrometry. Methods Enzymol 1990;193: 782–790.
   PubMed Web of Science ®Google Scholar
• Pomerantz Sc Fau, Pomerantz SC, McCloskey JA. Analysis of RNA hydrolyzates by liquid chromatography-mass spectrometry. Methods Enzymol 1990;193:796–824.
   Google Scholar
• Kubo K, Ide H, Wallace SS, Kow YW. A novel, sensitive, and specific assay for abasic sites, the most commonly produced DNA lesion. Biochemistry 1992;31:3703–3708.
   PubMed Web of Science ®Google Scholar
• Kojima N, Takebayashi T, Mikami A, Ohtsuka E, Komatsu Y. Construction of highly reactive probes for abasic site detection by introduction of an aromatic and a guanidine residue into an aminooxy group. J Am Chem Soc 2009; 131:13208–13209.
   Google Scholar
• Wrzesinski J, Szczepanik W, Ciesiolka J, Jezowska-Bojczuk M. tRNAPhe cleavage by aminoglycosides is triggered off by formation of an abasic site. Biochem Biophys Res Commun 2005;331:267–271.
   Google Scholar
• Kupfer PA, Crey-Desbiolles C, Leumann CJ. Trans-lesion synthesis and RNaseH activity by reverse transcriptases on a true abasic RNA template. Nucleic Acids Res 2007;35:6846–6853.
   Google Scholar
• Lindahl T, Nyberg B. Rate of depurination of native deoxyribonucleic acid. Biochemistry 1972;11:3610–3618.
   PubMed Web of Science ®Google Scholar
• Endo Y, Tsurugi K. RNA N-glycosidase activity of ricin A-chain. Mechanism of action of the toxic lectin ricin on eukaryotic ribosomes. J Biol Chem 1987;262:8128–8130.
   PubMed Web of Science ®Google Scholar
• Hudak KA, Bauman JD, Tumer NE. Pokeweed antiviral protein binds to the cap structure of eukaryotic mRNA and depurinates the mRNA downstream of the cap. RNA 2002; 8:1148–1159.
   Google Scholar
• Wu J, Li Z. Human polynucleotide phosphorylase reduces oxidative RNA damage and protects HeLa cell against oxidative stress. Biochem Biophys Res Commun 2008;372:288–292.
   PubMed Web of Science ®Google Scholar
• Hayakawa H, Kuwano M, Sekiguchi M. Specific binding of 8-oxoguanine-containing RNA to polynucleotide phosphorylase protein. Biochemistry 2001;40:9977–9982.
   Google Scholar
• Berquist BR, McNeill DR, Wilson DM, 3rd. Characterization of abasic endonuclease activity of human Ape1 on alternative substrates, as well as effects of ATP and sequence context on AP site incision. J Mol Biol 2008;379:17–27.
   PubMedGoogle Scholar
• Vascotto C, Fantini D, Romanello M, Cesaratto L, Deganuto M, Leonardi A, Radicella JP, Kelley MR, D'Ambrosio C, Scaloni A, Quadrifoglio F, Tell G. APE1/Ref-1 interacts with NPM1 within nucleoli and plays a role in the rRNA quality control process. Mol Cell Biol 2009;29:1834–1854.
   PubMed Web of Science ®Google Scholar
• Tanaka M, Chock PB, Stadtman ER. Oxidized messenger RNA induces translation errors. Proc Natl Acad Sci USA 2007;104:66–71.
   PubMed Web of Science ®Google Scholar
• Hudak KA, Wang P, Tumer NE. A novel mechanism for inhibition of translation by pokeweed antiviral protein: depurination of the capped RNA template. RNA 2000;6:369–380.
   Google Scholar
• Pang B, Zhou X, Yu H, Dong M, Taghizadeh K, Wishnok JS, Tannenbaum SR, Dedon PC. Lipid peroxidation dominates the chemistry of DNA adduct formation in a mouse model of inflammation. Carcinogenesis 2007;28:1807–1813.
   PubMedGoogle Scholar
• Nagayama T, Lan J, Henshall DC, Chen D, O'Horo C, Simon RP, Chen J. Induction of oxidative DNA damage in the peri-infarct region after permanent focal cerebral ischemia. J Neurochem 2000;75:1716–1728.
   PubMed Web of Science ®Google Scholar
• Kawai M, Saegusa Y, Dewa Y, Nishimura J, Kemmochi S, Harada T, Ishii Y, Umemura T, Shibutani M, Mitsumori K. Elevation of cell proliferation via generation of reactive oxygen species by piperonyl butoxide contributes to its liver tumor-promoting effects in mice. Arch Toxicol 2010;84: 155–164.
   Google Scholar
• Hickerson RP, Prat F, Muller JG, Foote CS, Burrows CJ. Sequence and stacking dependence of 8-oxoguanine oxidation: comparison of one-electron vs singlet oxygen mechanisms. J Am Chem Soc 1999;121:9423–9428.
   Web of Science ®Google Scholar